Job ID = 6627006 SRX = SRX8156259 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T00:19:03 prefetch.2.10.7: 1) Downloading 'SRR11588804'... 2020-07-14T00:19:03 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:19:51 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:19:52 prefetch.2.10.7: 'SRR11588804' is valid 2020-07-14T00:19:52 prefetch.2.10.7: 1) 'SRR11588804' was downloaded successfully Read 13932070 spots for SRR11588804/SRR11588804.sra Written 13932070 spots for SRR11588804/SRR11588804.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627149 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:27 13932070 reads; of these: 13932070 (100.00%) were unpaired; of these: 1924564 (13.81%) aligned 0 times 8788800 (63.08%) aligned exactly 1 time 3218706 (23.10%) aligned >1 times 86.19% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1679046 / 12007506 = 0.1398 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 09:28:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 09:28:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:28:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:28:18: 1000000 INFO @ Tue, 14 Jul 2020 09:28:25: 2000000 INFO @ Tue, 14 Jul 2020 09:28:31: 3000000 INFO @ Tue, 14 Jul 2020 09:28:37: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 09:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 09:28:42: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:28:42: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:28:44: 5000000 INFO @ Tue, 14 Jul 2020 09:28:49: 1000000 INFO @ Tue, 14 Jul 2020 09:28:50: 6000000 INFO @ Tue, 14 Jul 2020 09:28:56: 2000000 INFO @ Tue, 14 Jul 2020 09:28:57: 7000000 INFO @ Tue, 14 Jul 2020 09:29:03: 3000000 INFO @ Tue, 14 Jul 2020 09:29:04: 8000000 INFO @ Tue, 14 Jul 2020 09:29:10: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 09:29:10: 9000000 INFO @ Tue, 14 Jul 2020 09:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 09:29:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:29:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:29:16: 5000000 INFO @ Tue, 14 Jul 2020 09:29:17: 10000000 INFO @ Tue, 14 Jul 2020 09:29:19: 1000000 INFO @ Tue, 14 Jul 2020 09:29:19: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 09:29:19: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 09:29:19: #1 total tags in treatment: 10328460 INFO @ Tue, 14 Jul 2020 09:29:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:29:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:29:20: #1 tags after filtering in treatment: 10328460 INFO @ Tue, 14 Jul 2020 09:29:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:29:20: #1 finished! INFO @ Tue, 14 Jul 2020 09:29:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:29:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:29:20: #2 number of paired peaks: 101 WARNING @ Tue, 14 Jul 2020 09:29:20: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Tue, 14 Jul 2020 09:29:20: start model_add_line... INFO @ Tue, 14 Jul 2020 09:29:20: start X-correlation... INFO @ Tue, 14 Jul 2020 09:29:20: end of X-cor INFO @ Tue, 14 Jul 2020 09:29:20: #2 finished! INFO @ Tue, 14 Jul 2020 09:29:20: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 09:29:20: #2 alternative fragment length(s) may be 49,450,482,508,546 bps INFO @ Tue, 14 Jul 2020 09:29:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.05_model.r WARNING @ Tue, 14 Jul 2020 09:29:20: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:29:20: #2 You may need to consider one of the other alternative d(s): 49,450,482,508,546 WARNING @ Tue, 14 Jul 2020 09:29:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:29:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:29:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:29:23: 6000000 INFO @ Tue, 14 Jul 2020 09:29:26: 2000000 INFO @ Tue, 14 Jul 2020 09:29:30: 7000000 INFO @ Tue, 14 Jul 2020 09:29:32: 3000000 INFO @ Tue, 14 Jul 2020 09:29:37: 8000000 INFO @ Tue, 14 Jul 2020 09:29:39: 4000000 INFO @ Tue, 14 Jul 2020 09:29:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:29:43: 9000000 INFO @ Tue, 14 Jul 2020 09:29:46: 5000000 INFO @ Tue, 14 Jul 2020 09:29:50: 10000000 INFO @ Tue, 14 Jul 2020 09:29:52: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 09:29:52: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 09:29:52: #1 total tags in treatment: 10328460 INFO @ Tue, 14 Jul 2020 09:29:52: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:29:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:29:53: #1 tags after filtering in treatment: 10328460 INFO @ Tue, 14 Jul 2020 09:29:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:29:53: #1 finished! INFO @ Tue, 14 Jul 2020 09:29:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:29:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:29:53: 6000000 INFO @ Tue, 14 Jul 2020 09:29:53: #2 number of paired peaks: 101 WARNING @ Tue, 14 Jul 2020 09:29:53: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Tue, 14 Jul 2020 09:29:53: start model_add_line... INFO @ Tue, 14 Jul 2020 09:29:53: start X-correlation... INFO @ Tue, 14 Jul 2020 09:29:53: end of X-cor INFO @ Tue, 14 Jul 2020 09:29:53: #2 finished! INFO @ Tue, 14 Jul 2020 09:29:53: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 09:29:53: #2 alternative fragment length(s) may be 49,450,482,508,546 bps INFO @ Tue, 14 Jul 2020 09:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.10_model.r WARNING @ Tue, 14 Jul 2020 09:29:53: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:29:53: #2 You may need to consider one of the other alternative d(s): 49,450,482,508,546 WARNING @ Tue, 14 Jul 2020 09:29:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:29:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:29:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:29:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:29:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.05_summits.bed INFO @ Tue, 14 Jul 2020 09:29:54: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (408 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:29:59: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:30:05: 8000000 INFO @ Tue, 14 Jul 2020 09:30:12: 9000000 INFO @ Tue, 14 Jul 2020 09:30:16: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:30:18: 10000000 INFO @ Tue, 14 Jul 2020 09:30:20: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 09:30:20: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 09:30:20: #1 total tags in treatment: 10328460 INFO @ Tue, 14 Jul 2020 09:30:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:30:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:30:20: #1 tags after filtering in treatment: 10328460 INFO @ Tue, 14 Jul 2020 09:30:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:30:20: #1 finished! INFO @ Tue, 14 Jul 2020 09:30:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:30:21: #2 number of paired peaks: 101 WARNING @ Tue, 14 Jul 2020 09:30:21: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Tue, 14 Jul 2020 09:30:21: start model_add_line... INFO @ Tue, 14 Jul 2020 09:30:21: start X-correlation... INFO @ Tue, 14 Jul 2020 09:30:21: end of X-cor INFO @ Tue, 14 Jul 2020 09:30:21: #2 finished! INFO @ Tue, 14 Jul 2020 09:30:21: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 09:30:21: #2 alternative fragment length(s) may be 49,450,482,508,546 bps INFO @ Tue, 14 Jul 2020 09:30:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.20_model.r WARNING @ Tue, 14 Jul 2020 09:30:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:30:21: #2 You may need to consider one of the other alternative d(s): 49,450,482,508,546 WARNING @ Tue, 14 Jul 2020 09:30:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:30:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:30:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:30:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:30:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:30:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.10_summits.bed INFO @ Tue, 14 Jul 2020 09:30:28: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:30:44: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:30:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:30:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:30:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8156259/SRX8156259.20_summits.bed INFO @ Tue, 14 Jul 2020 09:30:55: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (57 records, 4 fields): 1 millis CompletedMACS2peakCalling